Jalal Alhalabi/Reuters

After weeks of vicious rebel infighting in northern Syria that has left more than a thousand dead and set jihadists at each other’s throats, al-Qaeda has disavowed the militant group triggering the war within Syria’s civil war, saying it isn’t responsible for the actions of the Islamic State of Iraq and Sham (ISIS). The disavowal—the first time the terror group’s top leadership has disowned an affiliate—takes al-Qaeda into unchartered territory.

Over the weekend, before al-Qaeda posted a brief statement on jihadi websites saying it was cutting links with the militant group led by Abu Bakr al-Baghdadi, who envisages carving out his own caliphate stretching across the Levant, ISIS fighters escalated the internecine strife by killing a senior Islamist commander in a suicide bomb targeting a rebel headquarters in the Syrian city of Aleppo.

The jihadist bomber had gained access using the ruse that he had come to negotiate a truce between the warring sides, say opposition activists. Among the dead were fighters from al-Qaeda affiliate Jabhat al-Nusra, which has supported ISIS’s opponents but has tried to stay on the sidelines of the rebel infighting.

Hours before al-Qaeda’s announcement renouncing ISIS, jihadi forums had been full of speculation that al-Qaeda’s leader, Ayman al-Zawahiri would disavow al-Baghdadi. When the statement came it was curt.

“Al-Qaeda announces that it does not link itself with (ISIS) ... It is not a branch of the al-Qaeda group, does not have an organizational relationship with it and (al-Qaeda) is not the group responsible for their actions,” the terror network’s General Command declared.

How the disavowal will play out on the ground and whether there will be a spike in defections from ISIS isn’t clear. Al-Baghdadi has been at loggerheads with al-Qaeda’s top leadership for months and has defied al-Zawahiri’s demand that he and his mainly foreign fighters leave Syria to Jabhat al-Nusra, which has close ties with Islamist rebels battling to topple Syrian President Bashar al-Assad. That order to leave Syria and for ISIS to focus on Iraq, where it has launched an offensive on the city of Fallujah, was cited in the General Command’s statement.

Analysts don’t expect the wayward al-Baghdadi to buckle under. Nothing in his past suggests he will. His mentor was Abu Mousab al-Zarqawi, a Jordanian militant who was rebuked by al-Zawahiri, then al-Qaeda’s top deputy, in 2005 for excessive extremism in Iraq. Al-Zarqawi, though, was never thrown out of al-Qaeda.

“This represents an attempt by core al-Qaeda to definitively re-assert some level of authority over the jihad in Syria. Tensions have existed within the jihadist movement in Syria since April 2013 and until now, core al-Qaeda has failed to take a genuinely commanding line,” says Charles Lister, a terrorism expert with the think tank Brookings Doha Center. “However, the outbreak of fighting between ISIS and other Syrian rebel groups on 3 January made it inevitable that Zawahiri would have to issue a decisive ruling with permanent consequences—and this is it.”

One of the reasons for the disavowal may be that al-Baghdadi’s defiance was beginning to threaten al-Zawahiri’s authority—top jihad scholars have over the past few weeks taken opposing sides in the dispute. Yesterday, an influential Saudi cleric, Abdullah bin Mohammed al-Moheisini, weighed in on the al-Qaeda’s chief side, issuing a statement about a peace plan to bring rebel infighting in northern Syria to a halt. In the statement, he made a plea to ISIS fighters to defect, suggesting they join Jabhat al-Nusra and Ahrar al-Sham, an Islamist brigade al-Qaeda helped form.

ISIS has been at the root of the internecine warfare between Syrian rebel groups. Both Western-backed insurgents and militants Islamist rebels suffered for months before full-blown infighting erupted from targeted abductions and assassinations by ISIS fighters.

ISIS has also been vicious with foes and civilians who live in territory it controls and who fail to observe its strict interpretation of Islam. It has resorted to beheadings and torture, say opposition activists and civilians who have escaped the group’s clutches.

Yesterday, ISIS posted a video online showing a fighter beheading a man as adults and children gathered to watch and in some cases cheer. In the video the fighter saws the man’s head off with a small knife. Some of the fighters are Russian-speaking and others a mix of non-Syrian Arabs and locals. According to Rami Abdurrahman of the Syrian Observatory of Human Rights, a UK-based prop-opposition group that has an extensive network of activists inside Syria, the decapitation probably occurred near the city of Homs last week.

In December, ISIS overstepped the mark with the assassination of rebel commander Ammar al-Wawi, prompting outrage in insurgent circles. Over the New Year the brutal ISIS killing of Dr. Hussein al-Suleiman, the leader of Ahrar al-Sham, one of the country’s biggest Islamist rebel groups that has links with al-Qaeda, was the final straw. Islamist rebels started to attack ISIS, with more moderate Free Syrian Army (FSA) brigades eventually joining in, and initially were successful in pushing the group out of the Syrian city of Aleppo and some other key rebel-held towns.

But early inroads against ISIS have now stalled and a strong counter-offensive by the group, along with a campaign of suicide bombings, confounded predictions that, with the array of different brigades challenging the jihadist group—from Western-backed moderates to hard-line Islamists—it would only be a matter of time before ISIS would be routed or at least severely diminished.

Although outnumbered—analysts estimate that al-Baghdadi commands from 10,000 to 15,000 fighters while Islamist brigades probably number around 40,000—ISIS has maintained its counter-punch. As well as launching the suicide bombing in Aleppo over the weekend, the group also ambushed the commander of the Suqour al-Sham group, Abu Hussein al-Dik, in Hama on Saturday.

The top al-Qaeda leadership has had trouble with wayward or over-ambitious members before, notably Algerian Mokhtar Belmokhtar, the one-eyed jihadist-turned-trafficker who oversaw a deadly raid and hostage standoff at an Algerian natural gas facility last year. But although he clashed with the core al-Qaeda leadership and defied their orders he wasn’t disavowed but broke away from al-Qaeda’s North Africa affiliate after being passed over for promotion, forming a group of his own called the “Signed in Blood” battalion.

Some analysts believe al-Baghdadi caused especial offense to core al-Qaeda by describing himself as “Emir of All Believers,” implying that he is the regional emir when al-Zawahiri has already appointed one—Aleppo-born Abu Khalid al-Suri, an al-Qaeda veteran, who plays a central role in the Islamist brigade Ahrar al-Sham. The disavowal is likely to isolate ISIS and could hinder its ability to recruit and fundraise in the Gulf, say analysts.

But terrorism expert Lister doesn’t think there will be an immediate ISIS collapse. “Inter-factional fighting in northern and eastern Syria is likely to continue, particularly in border areas and in and around key facilities and HQs of the variously involved groups.”

“All of this is damaging to the Syrian revolution,” Lister adds. “Any extent of inter-factional fighting simply represents the expenditure of valuable resources on objectives distinct from fighting the Assad government. So long as it continues, these inter-group hostilities make any kind of provincial, let alone national, opposition victory in Syria highly unlikely.”